We have continued our work related to developing methods to analyze molecular population genetic data. We have examined the performance of HapMap LD tag SNPs using the resequenced data of the Environmental Genome Project (EGP). We have introduced several algorithms to efficiently select linkage disequilibrium (LD) tag SNPs for genetic association studies. We developed 2 freely available software packages TAGster and mPopTag to select, evaluate and visualize LD tag SNPs both for single and multiple populations.